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- PDB-6eis: DYRK1A in complex with JWC-055 -

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Basic information

Entry
Database: PDB / ID: 6eis
TitleDYRK1A in complex with JWC-055
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1ADYRK1A
KeywordsTRANSFERASE / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / tau protein binding / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B6N / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 Å
AuthorsRothweiler, U.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors.
Authors: Czarna, A. / Wang, J. / Zelencova, D. / Liu, Y. / Deng, X. / Choi, H.G. / Zhang, T. / Zhou, W. / Chang, J.W. / Kildalsen, H. / Seternes, O.M. / Gray, N.S. / Engh, R.A. / Rothweiler, U.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,3138
Polymers170,6164
Non-polymers1,6974
Water6,107339
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0782
Polymers42,6541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0782
Polymers42,6541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0782
Polymers42,6541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0782
Polymers42,6541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.480, 89.050, 230.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dual specificity tyrosine-phosphorylation-regulated kinase 1A / DYRK1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


Mass: 42653.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase
#2: Chemical
ChemComp-B6N / 1-[4-fluoranyl-2-(trifluoromethyl)phenyl]-9-(1~{H}-pyrazol-4-yl)benzo[h][1,6]naphthyridin-2-one


Mass: 424.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H12F4N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M KSCN, 0.1M KCl, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 75870 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rrim(I) all: 0.13 / Net I/σ(I): 11.36
Reflection shellResolution: 2.36→2.5 Å / Mean I/σ(I) obs: 2.07 / Num. measured obs: 74036 / Num. unique all: 11965 / CC1/2: 0.722 / Rrim(I) all: 0.875

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementStarting model: 4nct

4nct


Resolution: 2.36→48.367 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.78
RfactorNum. reflection% reflection
Rfree0.2615 3757 4.95 %
Rwork0.221 --
obs0.223 75855 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.36→48.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11041 0 124 339 11504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311450
X-RAY DIFFRACTIONf_angle_d0.66915504
X-RAY DIFFRACTIONf_dihedral_angle_d13.9694274
X-RAY DIFFRACTIONf_chiral_restr0.0251647
X-RAY DIFFRACTIONf_plane_restr0.0031970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3559-2.38570.381180.34922553X-RAY DIFFRACTION96
2.3857-2.41710.41961190.32522652X-RAY DIFFRACTION100
2.4171-2.45020.39441270.32582665X-RAY DIFFRACTION100
2.4502-2.48520.35681350.31132605X-RAY DIFFRACTION100
2.4852-2.52230.35421380.30962665X-RAY DIFFRACTION100
2.5223-2.56170.39621440.31332616X-RAY DIFFRACTION100
2.5617-2.60370.3731410.31252648X-RAY DIFFRACTION100
2.6037-2.64860.35891480.3062611X-RAY DIFFRACTION100
2.6486-2.69680.32431190.30392693X-RAY DIFFRACTION100
2.6968-2.74870.36461880.2882578X-RAY DIFFRACTION100
2.7487-2.80480.38411480.29472652X-RAY DIFFRACTION100
2.8048-2.86570.28841170.2782690X-RAY DIFFRACTION100
2.8657-2.93240.3291220.2682639X-RAY DIFFRACTION100
2.9324-3.00570.29861540.26942637X-RAY DIFFRACTION100
3.0057-3.0870.31861320.25322679X-RAY DIFFRACTION100
3.087-3.17780.2817970.24522704X-RAY DIFFRACTION100
3.1778-3.28030.29521360.24742669X-RAY DIFFRACTION100
3.2803-3.39750.2731470.23042674X-RAY DIFFRACTION100
3.3975-3.53350.31161580.23512646X-RAY DIFFRACTION100
3.5335-3.69430.27181450.21662697X-RAY DIFFRACTION100
3.6943-3.8890.23311420.2052656X-RAY DIFFRACTION100
3.889-4.13250.21911180.17762703X-RAY DIFFRACTION100
4.1325-4.45140.19041530.16412709X-RAY DIFFRACTION100
4.4514-4.8990.19711320.15912710X-RAY DIFFRACTION100
4.899-5.6070.19771550.17732729X-RAY DIFFRACTION100
5.607-7.06070.20571400.19952765X-RAY DIFFRACTION100
7.0607-48.37750.21641840.18412853X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.1303 Å / Origin y: -7.3686 Å / Origin z: -28.3509 Å
111213212223313233
T0.3256 Å20.0279 Å2-0.0232 Å2-0.3002 Å2-0.0007 Å2--0.2892 Å2
L0.8261 °20.0684 °2-0.0595 °2-0.2941 °2-0.1581 °2--0.6336 °2
S0.0164 Å °0.2595 Å °-0.0055 Å °-0.0316 Å °-0.0166 Å °-0.0113 Å °-0.0338 Å °0.0884 Å °-0.0021 Å °
Refinement TLS groupSelection details: all

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